Development of an EST-SSR marker in Panax ginseng

2008 ◽  
Vol 5 (2) ◽  
pp. 175-181 ◽  
Author(s):  
Yang Cheng-Jun ◽  
Wang Jun ◽  
Mu Li-Qiang ◽  
Li Shao-Chen ◽  
Liu Guan-Jun ◽  
...  
Keyword(s):  
Panax Ginseng ◽  
Expressed Sequence Tags ◽  
Genomic Dna ◽  
Ssr Marker ◽  
Panax Quinquefolius ◽  
Chain Reaction ◽  
Acanthopanax Senticosus ◽  
Pcr Products ◽  
Polymerase Chain ◽  
Expressed Sequence

AbstractA total of 791 microsatellites (SSRs) were isolated from 7055 Panax ginseng expressed sequence tags (ESTs). According to primer design criteria, 68 primer pairs for EST-SSR were designed. Under an appropriate polymerase chain reaction (PCR) system, all EST-SSR primer pairs were screened against genomic DNA of Ji'anchangbo and Fusong'ermaya from Panax ginseng, and 43 EST-SSR primer pairs out of the above 68 resulted in PCR products. Then, all 43 pairs were detected in nine P. ginseng, two Panax quinquefolius and two Acanthopanax senticosus cultivars for polymorphisms, and 26 pairs (60.47%) were found to be polymorphic, accounting for 38.23% of the total number of designed primer pairs. These results demonstrate the possibility of developing EST-SSR markers using P. ginseng ESTs.

scholarly journals Assessment of molecular methods as a tool for detecting pathogenic protozoa isolated from water bodies

2015 ◽  
Vol 13 (4) ◽  
pp. 953-959 ◽  
Author(s):  
M. Adamska ◽  
M. Sawczuk ◽  
L. Kolodziejczyk ◽  
B. Skotarczak
Keyword(s):  
Water Samples ◽  
Genomic Dna ◽  
Water Bodies ◽  
Target Sequence ◽  
Chain Reaction ◽  
Four Seasons ◽  
Pcr Products ◽  
Polymerase Chain ◽  
North Western ◽  
Natural Water Bodies

Several species belong to the Cryptosporidium and Giardia genus, the main parasitic protozoa occurring in water, but only some of them are infectious to humans. We investigated the occurrence of Cryptosporidium and Giardia and identified their species in the water samples collected from natural water bodies in north-western Poland. A total of 600 samples from water bodies used for bathing, sewage discharge, as drinking water sources and watering places for animals were screened. The samples were collected during a 3-year period in each of the four seasons and filtered using Filta-Max (IDEXX Laboratories, USA). Genomic DNA was extracted from all samples and used as a target sequence for polymerase chain reaction (PCR) and TaqMan real-time PCR, as well as for reverse line blotting (RLB) methods. PCR methods seem to be more sensitive to detect Giardia and Cryptosporidium DNA in water samples than RLB methods. All PCR products were sequenced and three were identified as C. parvum and four as G. intestinalis. The overall prevalence of C. parvum (0.5%) and G. intestinalis (0.6%) in the samples suggests that the risk of Cryptosporidium and Giardia infections in north-western Poland is minimal.

scholarly journals Analysis of rearranged T-cell receptor beta-chain genes by polymerase chain reaction (PCR) DNA sequencing and automated high resolution PCR fragment analysis

Blood ◽  
1995 ◽  
Vol 86 (10) ◽  
pp. 3930-3937 ◽  
Author(s):  
M Kneba ◽  
I Bolz ◽  
B Linke ◽  
W Hiddemann
Keyword(s):  
Polymerase Chain Reaction ◽  
T Cell ◽  
High Resolution ◽  
Cell Lines ◽  
Genomic Dna ◽  
Lymphoblastic Leukemia ◽  
Chain Reaction ◽  
Pcr Products ◽  
Polymerase Chain ◽  
T Cell Lines

Polymerase chain reaction (PCR)-directed amplification and sequencing of rearranged immune genes for identification of clone-specific markers are increasingly being used in acute lymphoblastic leukemia (ALL) and non-Hodgkin's lymphoma (NHL) patients instead of the time consuming and labor intensive Southern analysis. In previous reports, no single common V beta and J beta sequence had been identified that allowed reliable amplification of the majority of rearranged T-cell antigen receptor (TCR)-beta V-D-J junctions at the DNA level because of the relatively large number of possible TCR-beta variable (V beta) and joining (J beta) gene segments involved in the rearrangement processes. In the present study we designed highly degenerate PCR primers directed against conserved sequences of the J beta genes. IN combination with a previously published consensus V beta primer, these J beta primers specifically amplify TCR- beta V-N(D)N-J junctions from genomic DNA. Using this approach we studied DNA extracted from biopsy material of nine patients with T-cell lymphoproliferative disorders, one c-ALL patient, and five patients with nonmalignant diseases. T-cell lines Molt 3, Jurkat, and HM 2 served as monoclonal controls. Individual PCR products were sequenced after cloning. The nucleotide sequences of 96 randomly chosen recombinant vectors were determined. In the polyclonal controls all analyzed clones differed in their TCR-beta V-N(D)N-J junctions. In the T-cell lines, in all of the T-cell malignancies, and in the c-ALL, monoclonal PCR products could be identified by demonstration of clonally restricted V-N(D)N-J junctions. The PCR results were confirmed by automated fluorescence quantification and size determination of PCR products after separation in a high- resolution polyacrylamide gel. The procedure allows rapid and specific characterization of clonal TCR-beta rearrangements from genomic DNA and will significantly simplify current experimental approaches to identify and to quantitate malignant T cells during initial staging and follow- up of T-lineage NHL and ALL patients.

Methodologies for Plasmopara halstedii Research

Helia ◽  
2019 ◽  
Vol 42 (71) ◽  
pp. 173-186
Author(s):  
Ana Laura Martínez ◽  
Freda Anderson ◽  
Facundo Quiroz ◽  
Antonio Garayalde ◽  
Ignacio Erreguerena ◽  
...  
Keyword(s):  
Expressed Sequence Tags ◽  
High Yield ◽  
Infected Leaf ◽  
Chain Reaction ◽  
Plasmopara Halstedii ◽  
Yield And Quality ◽  
Polymerase Chain ◽  
Expressed Sequence

Abstract The objective of this work was to find practical procedures to overcome methodological drawbacks encountered during studies on sunflower downy mildew. Techniques for recovering living isolates of Plasmopara halstedii from the field and for the preservation of infected leaf samples for further molecular analysis were developed. A Polymerase Chain Reaction (PCR)-based test for the detection of P. halstedii in sunflower leaves and a method to remove azoxystrobin from fungicide-treated seeds are proposed. In situ-inoculations of pre-germinated seeds allowed the recovery of living isolates from the field. Three sample-preservation methods were evaluated (silica, heating and lyophilization) resulting in high yield and quality of the DNA extract. It was detected the presence of the pathogen in symptomless leaves through PCR using molecular markers based on expressed sequence tags. A treatment using sodium hypochlorite is recommended for the removal of azoxystrobin from fungicide treated seeds.

scholarly journals A Comparative Study of 5S rDNA Non-Transcribed Spacers in Elaeagnaceae Species

Plants ◽  
2020 ◽  
Vol 10 (1) ◽  
pp. 4
Author(s):  
Oleg S. Alexandrov ◽  
Olga V. Razumova ◽  
Gennady I. Karlov
Keyword(s):  
Polymerase Chain Reaction ◽  
Molecular Markers ◽  
Dna Markers ◽  
5S Rdna ◽  
Chain Reaction ◽  
Closely Related Species ◽  
Pcr Products ◽  
Polymerase Chain ◽  
Species Specific ◽  
Shepherdia Canadensis

5S rDNA is organized as a cluster of tandemly repeated monomers that consist of the conservative 120 bp coding part and non-transcribed spacers (NTSs) with different lengths and sequences among different species. The polymorphism in the 5S rDNA NTSs of closely related species is interesting for phylogenetic and evolutional investigations, as well as for the development of molecular markers. In this study, the 5S rDNA NTSs were amplified with universal 5S1/5S2 primers in some species of the Elaeagnaceae Adans. family. The polymerase chain reaction (PCR) products of five Elaeagnus species had similar lengths near 310 bp and were different from Shepherdia canadensis (L.) Nutt. and Sh. argentea (Pusch.) Nutt. samples (260 bp and 215 bp, respectively). The PCR products were cloned and sequenced. An analysis of the sequences revealed that intraspecific levels of NTS identity are high (approximately 95–96%) and similar in the Elaeagnus L. species. In Sh. argentea, this level was slightly lower due to the differences in the poly-T region. Moreover, the intergeneric and intervarietal NTS identity levels were studied and compared. Significant differences between species (except E. multiflora Thunb. and E. umbellata Thunb.) and genera were found. Herein, a range of the NTS features is discussed. This study is another step in the investigation of the molecular evolution of Elaeagnaceae and may be useful for the development of species-specific DNA markers in this family.

Analysis of glutathione S-transferase genes polymorphisms and the risk of schizophrenia in a sample of Iranian population

2011 ◽  
Vol 7 (2-4) ◽  
pp. 199-203 ◽  
Author(s):  
Farah Lotfi Kashani ◽  
Dor Mohammad Kordi-Tamandani ◽  
Roya Sahranavard ◽  
Mohammad Hashemi ◽  
Farzaneh Kordi-Tamandani ◽  
...  
Keyword(s):  
Genomic Dna ◽  
Case Control Study ◽  
Gene Interaction ◽  
Case Control ◽  
Glutathione S Transferase ◽  
Chain Reaction ◽  
Healthy Control ◽  
Glutathione S Transferases ◽  
Polymerase Chain ◽  
Control Study

Glutathione S-transferases (GSTs) are major intracellular antioxidants, which, impaired in their function, are involved in the progress of schizophrenia (SCZ). The aim of this case-control study was to investigate the association between the polymorphism of glutathione S-transferases M1 (GSTM1), T1 (GSTT1), the glutathione S-transferase P1 gene (GSTP1) and SCZ. We isolated genomic DNA from peripheral blood of 93 individuals with SCZ and 99 healthy control subjects' genotypes analyzing them for GSTM1, GSTT1 and GSTP1 using polymerase chain reaction. The analysis of the gene–gene interaction between GSTs indicated that the magnitude of the association was greater for the combined AG/GSTT1 & GSTM1 genotypes (OR = 2.51; 95% CI: 1.13–5.63, P = 0.02). The AG and combined AG + GG genotypes of GSTP1 increased the risk of SCZ (OR = 1.83; 95% CI: 0.94–3.75 and OR = 1.71; 95% CI: 0.92–3.19, respectively). The genotypes of GSTT/NULL, NULL/GSTM and NULL/NULL increased the risk of SCZ (OR = 2.05; 95% CI: 0.9–4.74; OR = 2.0; 95% CI: 1.68–2.31; and OR = 1.8; 95% CI: 0.57–2.46, respectively). The present study supports previous data that suggest that impairment in the function of GSTs genes may increase the risk of SCZ.

Relationships among blueberry species within the section Cyanococcus of the Vaccinium genus based on EST-PCR markers

2021 ◽  
Author(s):  
Lisa Jeannine Rowland ◽  
Elizabeth L. Ogden ◽  
James R. Ballington
Keyword(s):  
Polymerase Chain Reaction ◽  
Expressed Sequence Tag ◽  
Clustering Methods ◽  
Polyploid Species ◽  
Pcr Markers ◽  
Chain Reaction ◽  
Ploidy Levels ◽  
Commercial Species ◽  
Polymerase Chain ◽  
Expressed Sequence

Commercial blueberry species of North America belong to the Vaccinium genus, section Cyanococcus. Phylogenetic relationships of 50 accessions of different ploidy levels within Cyanococcus were investigated using 249 expressed sequence tag-polymerase chain reaction markers and standard clustering methods. Of the commercial species, tetraploid V. corymbosum grouped most closely with the diploids, V. fuscatum and V. caesariense, followed by the diploid V. elliottii. Tetraploid V. angustifolium grouped with the diploids, V. boreale and V. myrtilloides. Hexaploid V. virgatum grouped most closely with the diploid V. tenellum, thus shedding light on the origins of these polyploid species.

scholarly journals Use of the polymerase chain reaction for detection of Fusarium graminearum in bulgur wheat

2012 ◽  
Vol 32 (1) ◽  
pp. 201-208 ◽  
Author(s):  
Carla Bertechini Faria ◽  
Giovana Caputo Almeida-Ferreira ◽  
Karina Bertechine Gagliardi ◽  
Tatiane Cristina Albuquerque Alves ◽  
Dauri José Tessmann ◽  
...  
Keyword(s):  
Polymerase Chain Reaction ◽  
Fusarium Graminearum ◽  
Genomic Dna ◽  
Solid Medium ◽  
Food Contamination ◽  
Chain Reaction ◽  
Specific Pcr ◽  
Culture Characteristics ◽  
Mycotoxigenic Fungi ◽  
Polymerase Chain

The detection of mycotoxigenic fungi in foodstuff is important because their presence may indicate the possible associated mycotoxin contamination. Fusarium graminearum is a wheat pathogen and a producer of micotoxins. The polymerase chain reaction (PCR) has been employed for the specific identification of F. graminearum. However, this methodology has not been commonly used for detection of F. graminearum in food. Thus, the objective of the present study was to develop a molecular methodology to detect F. graminearum in commercial samples of bulgur wheat. Two methods were tested. In the first method, a sample of this cereal was contaminated with F. graminearum mycelia. The genomic DNA was extracted from this mixture and used in a F. graminearum specific PCR reaction. The F. graminearum species was detected only in samples that were heavily contaminated. In the second method, samples of bulgur wheat were inoculated on a solid medium, and isolates having F. graminearum culture characteristics were obtained. The DNA extracted from these isolates was tested in F. graminearum specific PCR reactions. An isolate obtained had its trichothecene genotype identified by PCR. The established methodology could be used in surveys of food contamination with F. graminearum.

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